Clarke tweaked his left hamstring on Friday and it was always unlikely Australia would risk him, however selectors have produced a major shock by consigning the in-form batsman in the squad, Hughes, to 12th man duties.

Coach Darren Lehmann intimated on Saturday that Hughes, who has smashed two double centuries and an unbeaten ton for Australia A over the past six weeks, would come in and open alongside Aaron Finch should Clarke be ruled out.

However, with Clarke failing to prove his fitness, Brad Haddin will instead move to the top of the batting to partner Finch, leaving Australia’s middle order looking explosive but potentially vulnerable should they lose early wickets.

George Bailey will captain the side and likely bat at No3 with Steve Smith set to come in at second drop. After that, all-rounders Glenn Maxwell, Mitchell Marsh, James Faulkner and Mitchell Johnson will come in, followed by capable lower order hitters Mitchell Starc and Kane Richardson and then spinner Nathan Lyon.

Lehmann said in a statement late on Sunday that with Lyon picked for a Harare Sports Club deck noted for its turn, an extra all-rounder was included to “add further depth to our batting line-up.” However it seems unusual that Hughes would be left out if it was batting depth the side was after.

“Michael had a fitness test at training today and unfortunately hasn’t come through that well enough to be available for selection in game one,” said Lehmann. “He will continue intensive treatment on his hamstring and we’ll monitor his progress ahead of game two on Wednesday [against South Africa].

“Looking at the wicket today, we’ve opted to go with the spin option of Nathan Lyon along with the extra all-rounder to add further depth to our batting line-up which means that Phil Hughes has unfortunately missed out on selection.”

At a lengthy training session on Sunday, Clarke completed laps and shuttle runs as well as a net session – but walked away from an animated post-training meeting with Lehmann and selector Trevor Hohns shaking his head. Lehmann then entered into a long discussion with Bailey, before placing his arm around the shoulders of Hughes – who must have thought he was to return to international cricket for the first time in 12 months.

Clarke, who was clearly disappointed at being left out, will now race the clock in a bid to return for Wednesday’s second round-robin match against South Africa. Test spinner Lyon is back in the one-day squad for the first time since 2012.